Starting phenix.real_space_refine
on Sat Aug 23 10:31:45 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8j92_36085/08_2025/8j92_36085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j92_36085/08_2025/8j92_36085.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j92_36085/08_2025/8j92_36085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j92_36085/08_2025/8j92_36085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j92_36085/08_2025/8j92_36085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j92_36085/08_2025/8j92_36085.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     298      5.49       5
     S      14      5.16       5
     C    6641      2.51       5
     N    2226      2.21       5
     O    2824      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12003
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 794
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 665
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 794
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "D"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 716
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
    Chain: "E"
      Number of atoms: 793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 793
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 794
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 716
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 3037
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 3037
          Classifications: {'DNA': 149}
          Link IDs: {'rna3p': 148}
    Chain: "J"
      Number of atoms: 3072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 3072
          Classifications: {'DNA': 149}
          Link IDs: {'rna3p': 148}
  Time building chain proxies: 2.71, per 1000 atoms: 0.23
  Number of scatterers: 12003
  At special positions: 0
  Unit cell: (115.54, 121.9, 117.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     298     15.00
     O    2824      8.00
     N    2226      7.00
     C    6641      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 338.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1390

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      73.3% alpha, 2.9% beta
      129 base pairs and 260 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.538A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.808A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 25 through 31
    Processing helix  chain 'C' and resid 35 through 46
    Processing helix  chain 'C' and resid 55 through 82
    Processing helix  chain 'C' and resid 88 through 99
    Processing helix  chain 'C' and resid 99 through 106
    Processing helix  chain 'D' and resid 62 through 74
    Processing helix  chain 'D' and resid 80 through 107
      removed outlier: 3.537A  pdb=" N   LEU D 105 " --> pdb=" O   GLU D 101 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 110
      No H-bonds generated for 'chain 'D' and resid 108 through 110'
    Processing helix  chain 'D' and resid 115 through 127
    Processing helix  chain 'D' and resid 128 through 149
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 25 through 31
    Processing helix  chain 'G' and resid 35 through 46
    Processing helix  chain 'G' and resid 55 through 82
    Processing helix  chain 'G' and resid 88 through 99
    Processing helix  chain 'G' and resid 99 through 106
    Processing helix  chain 'H' and resid 62 through 74
    Processing helix  chain 'H' and resid 80 through 109
      removed outlier: 3.815A  pdb=" N   GLU H 101 " --> pdb=" O   LYS H  97 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 115 through 127
    Processing helix  chain 'H' and resid 128 through 149
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.159A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.805A  pdb=" N   THR B  96 " --> pdb=" O   THR G 110 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 52
      removed outlier: 7.004A  pdb=" N   ARG C  51 " --> pdb=" O   ILE D 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 87
    Processing sheet with id=AA6, first strand: chain 'C' and resid 110 through 111
      removed outlier: 7.105A  pdb=" N   THR C 110 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.315A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 51 through 52
      removed outlier: 7.182A  pdb=" N   ARG G  51 " --> pdb=" O   ILE H 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 86 through 87

    412 hydrogen bonds defined for protein.
    1224 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      332 hydrogen bonds
      664 hydrogen bond angles
      0 basepair planarities
      129 basepair parallelities
      260 stacking parallelities
  Total time for adding SS restraints: 2.10

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 2224
        1.33 -     1.45: 4271
        1.45 -     1.57: 5714
        1.57 -     1.69: 592
        1.69 -     1.81: 26
  Bond restraints: 12827
  Sorted by residual:
  bond pdb=" O3'  DA I -68 "
       pdb=" P    DG I -67 "
    ideal  model  delta    sigma   weight residual
    1.607  1.537  0.070 1.50e-02 4.44e+03 2.20e+01
  bond pdb=" O3'  DG I -73 "
       pdb=" P    DC I -72 "
    ideal  model  delta    sigma   weight residual
    1.607  1.546  0.061 1.50e-02 4.44e+03 1.64e+01
  bond pdb=" O3'  DT I -70 "
       pdb=" P    DG I -69 "
    ideal  model  delta    sigma   weight residual
    1.607  1.573  0.034 1.50e-02 4.44e+03 5.21e+00
  bond pdb=" O3'  DC I -72 "
       pdb=" P    DC I -71 "
    ideal  model  delta    sigma   weight residual
    1.607  1.579  0.028 1.50e-02 4.44e+03 3.41e+00
  bond pdb=" C2'  DA I -68 "
       pdb=" C1'  DA I -68 "
    ideal  model  delta    sigma   weight residual
    1.525  1.496  0.029 2.00e-02 2.50e+03 2.13e+00
  ... (remaining 12822 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 17979
        1.48 -     2.96: 561
        2.96 -     4.44: 42
        4.44 -     5.93: 9
        5.93 -     7.41: 3
  Bond angle restraints: 18594
  Sorted by residual:
  angle pdb=" O3'  DT I -70 "
        pdb=" C3'  DT I -70 "
        pdb=" C2'  DT I -70 "
      ideal   model   delta    sigma   weight residual
     111.50  106.64    4.86 1.50e+00 4.44e-01 1.05e+01
  angle pdb=" C4'  DG I -69 "
        pdb=" C3'  DG I -69 "
        pdb=" O3'  DG I -69 "
      ideal   model   delta    sigma   weight residual
     110.00  105.72    4.28 1.50e+00 4.44e-01 8.15e+00
  angle pdb=" C4'  DG I -74 "
        pdb=" O4'  DG I -74 "
        pdb=" C1'  DG I -74 "
      ideal   model   delta    sigma   weight residual
     109.70  105.70    4.00 1.50e+00 4.44e-01 7.10e+00
  angle pdb=" N   GLU D  96 "
        pdb=" CA  GLU D  96 "
        pdb=" CB  GLU D  96 "
      ideal   model   delta    sigma   weight residual
     110.16  114.05   -3.89 1.48e+00 4.57e-01 6.91e+00
  angle pdb=" C3'  DG J  20 "
        pdb=" C2'  DG J  20 "
        pdb=" C1'  DG J  20 "
      ideal   model   delta    sigma   weight residual
     101.60   97.70    3.90 1.50e+00 4.44e-01 6.75e+00
  ... (remaining 18589 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.69: 5433
       33.69 -    67.39: 1475
       67.39 -   101.08: 14
      101.08 -   134.77: 2
      134.77 -   168.46: 3
  Dihedral angle restraints: 6927
    sinusoidal: 4772
      harmonic: 2155
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   51.54  168.46     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" C4'  DC J -58 "
           pdb=" C3'  DC J -58 "
           pdb=" O3'  DC J -58 "
           pdb=" P    DT J -57 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   83.96  136.04     1      3.50e+01 8.16e-04 1.35e+01
  dihedral pdb=" C4'  DC J  34 "
           pdb=" C3'  DC J  34 "
           pdb=" O3'  DC J  34 "
           pdb=" P    DT J  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   84.70  135.30     1      3.50e+01 8.16e-04 1.34e+01
  ... (remaining 6924 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1488
       0.034 -    0.068: 507
       0.068 -    0.101: 94
       0.101 -    0.135: 28
       0.135 -    0.169: 4
  Chirality restraints: 2121
  Sorted by residual:
  chirality pdb=" CB  ILE H  79 "
            pdb=" CA  ILE H  79 "
            pdb=" CG1 ILE H  79 "
            pdb=" CG2 ILE H  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.15e-01
  chirality pdb=" C3'  DG I -74 "
            pdb=" C4'  DG I -74 "
            pdb=" O3'  DG I -74 "
            pdb=" C2'  DG I -74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.81    0.15 2.00e-01 2.50e+01 5.47e-01
  chirality pdb=" C3'  DT I -70 "
            pdb=" C4'  DT I -70 "
            pdb=" O3'  DT I -70 "
            pdb=" C2'  DT I -70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.81    0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 2118 not shown)

  Planarity restraints: 1312
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I -73 "    0.048 2.00e-02 2.50e+03   2.59e-02 2.02e+01
        pdb=" N9   DG I -73 "   -0.015 2.00e-02 2.50e+03
        pdb=" C8   DG I -73 "   -0.011 2.00e-02 2.50e+03
        pdb=" N7   DG I -73 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I -73 "   -0.031 2.00e-02 2.50e+03
        pdb=" C6   DG I -73 "   -0.030 2.00e-02 2.50e+03
        pdb=" O6   DG I -73 "    0.056 2.00e-02 2.50e+03
        pdb=" N1   DG I -73 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DG I -73 "    0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I -73 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DG I -73 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DG I -73 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I -69 "   -0.025 2.00e-02 2.50e+03   1.57e-02 7.39e+00
        pdb=" N9   DG I -69 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DG I -69 "    0.014 2.00e-02 2.50e+03
        pdb=" N7   DG I -69 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I -69 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DG I -69 "   -0.027 2.00e-02 2.50e+03
        pdb=" O6   DG I -69 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1   DG I -69 "    0.020 2.00e-02 2.50e+03
        pdb=" C2   DG I -69 "   -0.008 2.00e-02 2.50e+03
        pdb=" N2   DG I -69 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I -69 "    0.008 2.00e-02 2.50e+03
        pdb=" C4   DG I -69 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I -70 "   -0.014 2.00e-02 2.50e+03   1.35e-02 4.59e+00
        pdb=" N1   DT I -70 "    0.034 2.00e-02 2.50e+03
        pdb=" C2   DT I -70 "   -0.013 2.00e-02 2.50e+03
        pdb=" O2   DT I -70 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DT I -70 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DT I -70 "   -0.013 2.00e-02 2.50e+03
        pdb=" O4   DT I -70 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DT I -70 "    0.004 2.00e-02 2.50e+03
        pdb=" C7   DT I -70 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DT I -70 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1309 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2219
        2.79 -     3.32: 10426
        3.32 -     3.84: 23617
        3.84 -     4.37: 27847
        4.37 -     4.90: 39494
  Nonbonded interactions: 103603
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  27 "
            pdb=" O   LEU G  32 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OG  SER C  27 "
            pdb=" O   LEU C  32 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" ND2 ASN E 108 "
            pdb=" O   GLY F  42 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH1 ARG A 131 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.306 3.120
  ... (remaining 103598 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 39 through 134)
  selection = (chain 'E' and resid 39 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.190
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  12827  Z= 0.197
  Angle     :  0.583   7.407  18594  Z= 0.351
  Chirality :  0.036   0.169   2121
  Planarity :  0.004   0.044   1312
  Dihedral  : 28.059 168.462   5537
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.70 (0.30), residues: 733
  helix:  2.45 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.24 (0.42), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  49 
 TYR   0.011   0.002   TYR H  65 
 PHE   0.011   0.001   PHE D  90 
 HIS   0.009   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (12827)
  covalent geometry    : angle       0.58321 (18594)
  hydrogen bonds       : bond        0.07540 (  744)
  hydrogen bonds       : angle       3.41646 ( 1888)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8181 (mt-10)
REVERT: B   84 MET cc_start: 0.7771 (mmm) cc_final: 0.7461 (tpp)
REVERT: C   81 ASP cc_start: 0.7890 (m-30) cc_final: 0.7683 (m-30)
REVERT: D   72 GLN cc_start: 0.7555 (tt0) cc_final: 0.7206 (tt0)
REVERT: G   84 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8358 (mmmm)
REVERT: G  104 LYS cc_start: 0.7996 (tttt) cc_final: 0.7735 (mtpt)
REVERT: H  147 THR cc_start: 0.7267 (m) cc_final: 0.7030 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.9168
  time to fit residues: 167.6466
Evaluate side-chains
  100 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0370
   overall best weight:    0.7460

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN
D 109 ASN
D 120 GLN
E 108 ASN
F  25 ASN
G  33 GLN
H  72 GLN
H 109 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.177735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.128621 restraints weight = 13253.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 0.85
r_work: 0.3229 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12827  Z= 0.153
  Angle     :  0.539   6.254  18594  Z= 0.327
  Chirality :  0.033   0.134   2121
  Planarity :  0.004   0.038   1312
  Dihedral  : 30.903 170.828   4065
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 12.54 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.10 (0.31), residues: 733
  helix:  2.73 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.01 (0.43), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  83 
 TYR   0.011   0.001   TYR C  66 
 PHE   0.007   0.001   PHE H 146 
 HIS   0.004   0.001   HIS H 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (12827)
  covalent geometry    : angle       0.53883 (18594)
  hydrogen bonds       : bond        0.04009 (  744)
  hydrogen bonds       : angle       2.72482 ( 1888)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8180 (ttmm)
REVERT: A  115 LYS cc_start: 0.8570 (mptp) cc_final: 0.8256 (mttm)
REVERT: A  120 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8004 (mtt)
REVERT: B   84 MET cc_start: 0.8624 (mmm) cc_final: 0.8397 (tpp)
REVERT: C   70 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7937 (tp30)
REVERT: D   72 GLN cc_start: 0.7979 (tt0) cc_final: 0.7686 (tt0)
REVERT: D  111 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8426 (mmtp)
REVERT: D  118 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8158 (mp0)
REVERT: G   82 ASN cc_start: 0.7903 (t0) cc_final: 0.7462 (t0)
REVERT: G   84 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8514 (mmmm)
REVERT: H   96 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7266 (mp0)
REVERT: H  147 THR cc_start: 0.7159 (m) cc_final: 0.6925 (p)
  outliers start: 20
  outliers final: 7
  residues processed: 124
  average time/residue: 0.8659
  time to fit residues: 113.6502
Evaluate side-chains
  119 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain C residue   70 GLU
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  111 LYS
Chi-restraints excluded: chain D residue  118 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   50 GLN
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   96 GLU
Chi-restraints excluded: chain H residue  118 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 83 optimal weight:    8.9990
   chunk 85 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
D  74 HIS
F  25 ASN
G  33 GLN
H 109 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.169355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.119199 restraints weight = 13321.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 0.85
r_work: 0.3100 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12827  Z= 0.232
  Angle     :  0.618   6.542  18594  Z= 0.365
  Chirality :  0.038   0.178   2121
  Planarity :  0.005   0.045   1312
  Dihedral  : 31.324 169.667   4065
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 14.79 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.43 (0.30), residues: 733
  helix:  2.24 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.32 (0.43), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  80 
 TYR   0.017   0.002   TYR F  51 
 PHE   0.014   0.002   PHE A  78 
 HIS   0.003   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 (12827)
  covalent geometry    : angle       0.61829 (18594)
  hydrogen bonds       : bond        0.05213 (  744)
  hydrogen bonds       : angle       2.96256 ( 1888)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 122
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8357 (ttmm)
REVERT: A  129 ARG cc_start: 0.7909 (tpt90) cc_final: 0.7672 (tpt-90)
REVERT: B   59 LYS cc_start: 0.8676 (tttm) cc_final: 0.8328 (ttpp)
REVERT: D   72 GLN cc_start: 0.7838 (tt0) cc_final: 0.7540 (tt0)
REVERT: D   96 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7644 (tp30)
REVERT: D  111 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8395 (mmtp)
REVERT: F   88 TYR cc_start: 0.9192 (m-10) cc_final: 0.8917 (m-10)
REVERT: F   92 ARG cc_start: 0.8353 (mtp85) cc_final: 0.8026 (mtp85)
REVERT: G   82 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7571 (t0)
REVERT: G   84 LYS cc_start: 0.8784 (mmtm) cc_final: 0.8551 (mmtp)
REVERT: H   96 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7484 (mp0)
REVERT: H  104 LYS cc_start: 0.7720 (ptpt) cc_final: 0.7431 (mtmt)
REVERT: H  111 LYS cc_start: 0.7708 (tttp) cc_final: 0.7165 (mmtm)
REVERT: H  147 THR cc_start: 0.7258 (m) cc_final: 0.6979 (p)
  outliers start: 30
  outliers final: 6
  residues processed: 137
  average time/residue: 0.9218
  time to fit residues: 133.0115
Evaluate side-chains
  127 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain D residue   96 GLU
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  111 LYS
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain G residue   82 ASN
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   96 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 93 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D 120 GLN
E 108 ASN
F  25 ASN
G  33 GLN
H 109 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.170107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.119981 restraints weight = 13267.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 0.83
r_work: 0.3120 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12827  Z= 0.192
  Angle     :  0.567   5.820  18594  Z= 0.340
  Chirality :  0.035   0.142   2121
  Planarity :  0.004   0.041   1312
  Dihedral  : 31.032 167.944   4065
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 17.04 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.30), residues: 733
  helix:  2.28 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.28 (0.43), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  69 
 TYR   0.013   0.002   TYR F  51 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (12827)
  covalent geometry    : angle       0.56660 (18594)
  hydrogen bonds       : bond        0.04452 (  744)
  hydrogen bonds       : angle       2.88070 ( 1888)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8277 (ttmm)
REVERT: A  129 ARG cc_start: 0.7902 (tpt90) cc_final: 0.7661 (tpt-90)
REVERT: B   68 ASP cc_start: 0.8869 (m-30) cc_final: 0.8461 (m-30)
REVERT: D   72 GLN cc_start: 0.7760 (tt0) cc_final: 0.7460 (tt0)
REVERT: D  111 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8375 (mmtp)
REVERT: D  118 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8323 (mp0)
REVERT: E   49 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7817 (mtm110)
REVERT: E   56 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8128 (ttmt)
REVERT: F   92 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7859 (mtp85)
REVERT: G   82 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7622 (t0)
REVERT: G   84 LYS cc_start: 0.8782 (mmtm) cc_final: 0.8525 (mmtp)
REVERT: H   96 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7571 (mp0)
REVERT: H  104 LYS cc_start: 0.7481 (ptpt) cc_final: 0.7262 (mtmt)
REVERT: H  107 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7272 (ttm110)
REVERT: H  111 LYS cc_start: 0.7645 (tttp) cc_final: 0.7133 (mmtm)
  outliers start: 27
  outliers final: 11
  residues processed: 128
  average time/residue: 0.7865
  time to fit residues: 106.0041
Evaluate side-chains
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  111 LYS
Chi-restraints excluded: chain D residue  118 GLU
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   50 GLN
Chi-restraints excluded: chain G residue   82 ASN
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue   71 LYS
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   96 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 90 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 88 optimal weight:    7.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
G  33 GLN
H 109 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.170869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.120876 restraints weight = 13321.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 0.82
r_work: 0.3126 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12827  Z= 0.171
  Angle     :  0.557   5.345  18594  Z= 0.336
  Chirality :  0.034   0.141   2121
  Planarity :  0.004   0.041   1312
  Dihedral  : 31.028 168.450   4065
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 18.49 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.59 (0.30), residues: 733
  helix:  2.36 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.27 (0.43), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  83 
 TYR   0.012   0.002   TYR F  51 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (12827)
  covalent geometry    : angle       0.55736 (18594)
  hydrogen bonds       : bond        0.04283 (  744)
  hydrogen bonds       : angle       2.85719 ( 1888)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8246 (ttmm)
REVERT: A  115 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8208 (mptp)
REVERT: A  129 ARG cc_start: 0.7902 (tpt90) cc_final: 0.7661 (tpt-90)
REVERT: B   68 ASP cc_start: 0.8844 (m-30) cc_final: 0.8461 (m-30)
REVERT: D   72 GLN cc_start: 0.7762 (tt0) cc_final: 0.7464 (tt0)
REVERT: D  111 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8373 (mmtp)
REVERT: D  118 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8313 (mp0)
REVERT: F   92 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7922 (ttm-80)
REVERT: G   82 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7621 (t0)
REVERT: G   84 LYS cc_start: 0.8777 (mmtm) cc_final: 0.8518 (mmtp)
REVERT: H   96 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7617 (mp0)
REVERT: H  111 LYS cc_start: 0.7629 (tttp) cc_final: 0.7097 (mmtm)
  outliers start: 25
  outliers final: 10
  residues processed: 125
  average time/residue: 0.8667
  time to fit residues: 114.0285
Evaluate side-chains
  126 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  111 LYS
Chi-restraints excluded: chain D residue  118 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   50 GLN
Chi-restraints excluded: chain G residue   82 ASN
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue   71 LYS
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   96 GLU
Chi-restraints excluded: chain H residue  147 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 73 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 75 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
H  74 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.170357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.119582 restraints weight = 13322.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 0.84
r_work: 0.3105 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12827  Z= 0.179
  Angle     :  0.553   5.301  18594  Z= 0.332
  Chirality :  0.034   0.132   2121
  Planarity :  0.004   0.041   1312
  Dihedral  : 30.977 167.924   4065
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 17.68 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.61 (0.30), residues: 733
  helix:  2.40 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.32 (0.42), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  35 
 TYR   0.012   0.002   TYR F  51 
 PHE   0.011   0.001   PHE A  67 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (12827)
  covalent geometry    : angle       0.55330 (18594)
  hydrogen bonds       : bond        0.04318 (  744)
  hydrogen bonds       : angle       2.83003 ( 1888)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8246 (ttmm)
REVERT: A  115 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8317 (mptp)
REVERT: A  129 ARG cc_start: 0.7926 (tpt90) cc_final: 0.7659 (tpt-90)
REVERT: B   68 ASP cc_start: 0.8808 (m-30) cc_final: 0.8449 (m-30)
REVERT: D   72 GLN cc_start: 0.7786 (tt0) cc_final: 0.7482 (tt0)
REVERT: D  111 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8310 (mmtp)
REVERT: D  118 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8251 (mp0)
REVERT: G   82 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7633 (t0)
REVERT: G   84 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8469 (mmtp)
REVERT: H   96 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7516 (mp0)
REVERT: H  100 SER cc_start: 0.9122 (p) cc_final: 0.8784 (m)
REVERT: H  107 ARG cc_start: 0.7459 (mtm-85) cc_final: 0.7013 (mtm110)
REVERT: H  111 LYS cc_start: 0.7580 (tttp) cc_final: 0.7038 (mmtm)
REVERT: H  118 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7759 (mp0)
  outliers start: 28
  outliers final: 12
  residues processed: 131
  average time/residue: 0.8538
  time to fit residues: 117.9760
Evaluate side-chains
  132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  111 LYS
Chi-restraints excluded: chain D residue  118 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   50 GLN
Chi-restraints excluded: chain G residue   82 ASN
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue   71 LYS
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   96 GLU
Chi-restraints excluded: chain H residue  118 GLU
Chi-restraints excluded: chain H residue  147 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 85 optimal weight:   10.0000
   chunk 42 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
D 120 GLN
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.171036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.120869 restraints weight = 13303.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 0.88
r_work: 0.3112 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.3109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12827  Z= 0.155
  Angle     :  0.538   5.129  18594  Z= 0.326
  Chirality :  0.033   0.141   2121
  Planarity :  0.004   0.041   1312
  Dihedral  : 30.961 167.622   4065
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.29 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.77 (0.30), residues: 733
  helix:  2.52 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.28 (0.43), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  80 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (12827)
  covalent geometry    : angle       0.53809 (18594)
  hydrogen bonds       : bond        0.04075 (  744)
  hydrogen bonds       : angle       2.82907 ( 1888)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8209 (ttmm)
REVERT: A  115 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8197 (mptp)
REVERT: A  129 ARG cc_start: 0.7938 (tpt90) cc_final: 0.7674 (tpt-90)
REVERT: B   68 ASP cc_start: 0.8812 (m-30) cc_final: 0.8471 (m-30)
REVERT: D   72 GLN cc_start: 0.7779 (tt0) cc_final: 0.7496 (tt0)
REVERT: D  111 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8322 (mmtp)
REVERT: G   82 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7617 (t0)
REVERT: G   84 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8448 (mmtp)
REVERT: H   96 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7560 (mp0)
REVERT: H  100 SER cc_start: 0.9164 (p) cc_final: 0.8822 (m)
REVERT: H  111 LYS cc_start: 0.7577 (tttp) cc_final: 0.7054 (mmtm)
REVERT: H  118 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7731 (mp0)
  outliers start: 21
  outliers final: 9
  residues processed: 126
  average time/residue: 0.8012
  time to fit residues: 106.7526
Evaluate side-chains
  128 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  111 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   82 ASN
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   96 GLU
Chi-restraints excluded: chain H residue  118 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 88 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
H  74 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.166415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.115764 restraints weight = 13261.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 0.88
r_work: 0.3039 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  12827  Z= 0.274
  Angle     :  0.650   6.751  18594  Z= 0.378
  Chirality :  0.040   0.188   2121
  Planarity :  0.005   0.041   1312
  Dihedral  : 31.384 166.617   4065
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 18.33 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.30), residues: 733
  helix:  2.02 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.48 (0.42), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  36 
 TYR   0.019   0.003   TYR E  54 
 PHE   0.013   0.003   PHE A  78 
 HIS   0.004   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 (12827)
  covalent geometry    : angle       0.65039 (18594)
  hydrogen bonds       : bond        0.05590 (  744)
  hydrogen bonds       : angle       3.04882 ( 1888)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8413 (ttmm)
REVERT: A   59 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7328 (pt0)
REVERT: A  115 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8351 (mptp)
REVERT: A  129 ARG cc_start: 0.7981 (tpt90) cc_final: 0.7684 (tpt-90)
REVERT: B   59 LYS cc_start: 0.8682 (tttm) cc_final: 0.8288 (ttpp)
REVERT: B   68 ASP cc_start: 0.8904 (m-30) cc_final: 0.8490 (m-30)
REVERT: B   79 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8546 (mtmm)
REVERT: C  101 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7617 (mt-10)
REVERT: D   72 GLN cc_start: 0.7859 (tt0) cc_final: 0.7489 (tt0)
REVERT: D  138 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7924 (mm-30)
REVERT: G   82 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7815 (t0)
REVERT: G   84 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8421 (mmtp)
REVERT: H   96 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7491 (mp0)
REVERT: H  109 ASN cc_start: 0.8359 (m-40) cc_final: 0.8158 (m-40)
REVERT: H  111 LYS cc_start: 0.8049 (tttp) cc_final: 0.7371 (mmtm)
  outliers start: 27
  outliers final: 12
  residues processed: 129
  average time/residue: 0.8705
  time to fit residues: 118.2792
Evaluate side-chains
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue  101 GLU
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain G residue   82 ASN
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue   71 LYS
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   96 GLU
Chi-restraints excluded: chain H residue  147 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 84 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 88 optimal weight:    7.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    2.1584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G  33 GLN
H  72 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.167907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.117156 restraints weight = 13207.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 0.82
r_work: 0.3072 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12827  Z= 0.214
  Angle     :  0.590   5.693  18594  Z= 0.350
  Chirality :  0.036   0.198   2121
  Planarity :  0.005   0.043   1312
  Dihedral  : 31.174 165.763   4065
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.94 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.30), residues: 733
  helix:  2.15 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.43 (0.42), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  69 
 TYR   0.014   0.002   TYR F  51 
 PHE   0.012   0.002   PHE A  67 
 HIS   0.003   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (12827)
  covalent geometry    : angle       0.59005 (18594)
  hydrogen bonds       : bond        0.04799 (  744)
  hydrogen bonds       : angle       2.94848 ( 1888)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8337 (ttmm)
REVERT: A   59 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7321 (pt0)
REVERT: A  115 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8333 (mptp)
REVERT: A  129 ARG cc_start: 0.7939 (tpt90) cc_final: 0.7643 (tpt-90)
REVERT: B   68 ASP cc_start: 0.8866 (m-30) cc_final: 0.8491 (m-30)
REVERT: D   72 GLN cc_start: 0.7806 (tt0) cc_final: 0.7450 (tt0)
REVERT: D  138 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7891 (mm-30)
REVERT: G   80 ARG cc_start: 0.7381 (ttm110) cc_final: 0.6818 (ttm-80)
REVERT: G   82 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7765 (t0)
REVERT: G   84 LYS cc_start: 0.8724 (mmtm) cc_final: 0.8423 (mmtp)
REVERT: H   96 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7535 (mp0)
REVERT: H  110 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8240 (mtpp)
REVERT: H  111 LYS cc_start: 0.7901 (tttp) cc_final: 0.7249 (mmtm)
  outliers start: 21
  outliers final: 12
  residues processed: 121
  average time/residue: 0.8896
  time to fit residues: 113.4651
Evaluate side-chains
  126 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain G residue   82 ASN
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue   71 LYS
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   96 GLU
Chi-restraints excluded: chain H residue  110 LYS
Chi-restraints excluded: chain H residue  147 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 9 optimal weight:    0.6980
   chunk 19 optimal weight:    6.9990
   chunk 85 optimal weight:   10.0000
   chunk 42 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 76 optimal weight:    7.9990
   chunk 82 optimal weight:    7.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
G  33 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.169357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.118876 restraints weight = 13337.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 0.85
r_work: 0.3091 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12827  Z= 0.157
  Angle     :  0.554   5.573  18594  Z= 0.335
  Chirality :  0.034   0.173   2121
  Planarity :  0.004   0.042   1312
  Dihedral  : 31.143 166.217   4065
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 20.10 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.56 (0.30), residues: 733
  helix:  2.37 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.35 (0.43), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.012   0.002   TYR F  51 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (12827)
  covalent geometry    : angle       0.55437 (18594)
  hydrogen bonds       : bond        0.04230 (  744)
  hydrogen bonds       : angle       2.89830 ( 1888)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8227 (ttmm)
REVERT: A   59 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7302 (pt0)
REVERT: A  115 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8194 (mptp)
REVERT: A  129 ARG cc_start: 0.7924 (tpt90) cc_final: 0.7652 (tpt-90)
REVERT: B   68 ASP cc_start: 0.8851 (m-30) cc_final: 0.8478 (m-30)
REVERT: B   79 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8528 (mtmm)
REVERT: D   72 GLN cc_start: 0.7754 (tt0) cc_final: 0.7425 (tt0)
REVERT: G   80 ARG cc_start: 0.7380 (ttm110) cc_final: 0.6823 (ttm-80)
REVERT: G   84 LYS cc_start: 0.8718 (mmtm) cc_final: 0.8421 (mmtp)
REVERT: H   96 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7570 (mp0)
REVERT: H  100 SER cc_start: 0.9132 (p) cc_final: 0.8778 (m)
REVERT: H  110 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8247 (mtpp)
REVERT: H  111 LYS cc_start: 0.7888 (tttp) cc_final: 0.7261 (mmtm)
  outliers start: 21
  outliers final: 11
  residues processed: 123
  average time/residue: 0.8870
  time to fit residues: 115.0396
Evaluate side-chains
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue   71 LYS
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   96 GLU
Chi-restraints excluded: chain H residue  110 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 81 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9980
   chunk 76 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 23 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G  33 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.168310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.118014 restraints weight = 13312.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 0.88
r_work: 0.3064 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12827  Z= 0.200
  Angle     :  0.579   5.780  18594  Z= 0.344
  Chirality :  0.036   0.181   2121
  Planarity :  0.005   0.043   1312
  Dihedral  : 31.125 166.886   4065
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.26 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.30), residues: 733
  helix:  2.26 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.38 (0.43), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  69 
 TYR   0.014   0.002   TYR F  51 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (12827)
  covalent geometry    : angle       0.57880 (18594)
  hydrogen bonds       : bond        0.04687 (  744)
  hydrogen bonds       : angle       2.93414 ( 1888)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4386.57 seconds
wall clock time: 75 minutes 8.34 seconds (4508.34 seconds total)